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- PDB-3q1c: Structure of EspG Protein -

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Basic information

Entry
Database: PDB / ID: 3q1c
TitleStructure of EspG Protein
ComponentsLEE-encoded effector EspG
KeywordsSIGNALING PROTEIN / VirA fold / virulence factor / PAK recruitment and activation / p21 activated kinase
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
LEE-encoded effector EspG
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.596 Å
AuthorsSpiller, B.W. / Germane, K.L.
CitationJournal: Biochemistry / Year: 2011
Title: Structural and Functional Studies Indicate That the EPEC Effector, EspG, Directly Binds p21-Activated Kinase.
Authors: Germane, K.L. / Spiller, B.W.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEE-encoded effector EspG


Theoretical massNumber of molelcules
Total (without water)39,8801
Polymers39,8801
Non-polymers00
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.150, 74.378, 93.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LEE-encoded effector EspG / EPEC virulence factor


Mass: 39879.578 Da / Num. of mol.: 1 / Fragment: UNP residues 44-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Strain: E2348/69 / EPEC / Gene: E2348C_3970, E2348_C_3970, espG
Plasmid details: An N-terminal 6His tag was cleaved with Thrombin.
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7UMC8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 2.0-11.0% PEG8000, 100 mM Bis-Tris, pH 6.25-7.5, VAPOR DIFFUSION, HANGING DROP, temperature range 268-291K
PH range: 6.25-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.595→32.958 Å / Num. obs: 60098 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 32
Reflection shell
Resolution (Å)
1.6-1.66
1.66-1.72
1.72-1.8
1.8-1.9
1.9-2.02
2.02-2.17
2.17-2.39
2.39-2.74
2.74-3.45
3.45-50

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.596→32.093 Å / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1881 1959 3.35 %
Rwork0.1613 --
obs0.1622 58526 87.43 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.988 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9506 Å20 Å2-0 Å2
2--3.9669 Å20 Å2
3----3.0164 Å2
Refine analyzeLuzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.596→32.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 0 446 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062766
X-RAY DIFFRACTIONf_angle_d0.9673755
X-RAY DIFFRACTIONf_dihedral_angle_d13.7621036
X-RAY DIFFRACTIONf_chiral_restr0.07434
X-RAY DIFFRACTIONf_plane_restr0.004493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5957-1.63560.3183770.2221978X-RAY DIFFRACTION43
1.6356-1.67980.2593830.20162415X-RAY DIFFRACTION53
1.6798-1.72920.26931000.15312951X-RAY DIFFRACTION65
1.7292-1.7850.17211260.13833888X-RAY DIFFRACTION85
1.785-1.84880.14531480.12354296X-RAY DIFFRACTION94
1.8488-1.92290.19661500.13364396X-RAY DIFFRACTION96
1.9229-2.01040.15951550.13714455X-RAY DIFFRACTION97
2.0104-2.11630.19231610.14354490X-RAY DIFFRACTION98
2.1163-2.24890.16281540.14734533X-RAY DIFFRACTION98
2.2489-2.42250.18211540.15284551X-RAY DIFFRACTION99
2.4225-2.66610.19341600.16024593X-RAY DIFFRACTION99
2.6661-3.05170.23471660.17214612X-RAY DIFFRACTION99
3.0517-3.84380.17091620.1614688X-RAY DIFFRACTION99
3.8438-32.09940.18431630.18284721X-RAY DIFFRACTION97

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